Multiple sequence alignment - TraesCS7D01G183700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G183700 chr7D 100.000 1864 0 0 860 2723 137293733 137291870 0.000000e+00 3443
1 TraesCS7D01G183700 chr7D 100.000 574 0 0 1 574 137294592 137294019 0.000000e+00 1061
2 TraesCS7D01G183700 chr7B 92.741 1901 63 8 865 2723 101497690 101495823 0.000000e+00 2676
3 TraesCS7D01G183700 chr7B 93.924 576 29 4 1 573 101498403 101497831 0.000000e+00 865
4 TraesCS7D01G183700 chr7A 93.705 1795 60 8 865 2623 137453392 137451615 0.000000e+00 2639
5 TraesCS7D01G183700 chr7A 91.622 370 28 3 1 369 137454173 137453806 2.420000e-140 508
6 TraesCS7D01G183700 chr7A 91.000 200 14 4 376 573 137453725 137453528 1.610000e-67 267


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G183700 chr7D 137291870 137294592 2722 True 2252.0 3443 100.0000 1 2723 2 chr7D.!!$R1 2722
1 TraesCS7D01G183700 chr7B 101495823 101498403 2580 True 1770.5 2676 93.3325 1 2723 2 chr7B.!!$R1 2722
2 TraesCS7D01G183700 chr7A 137451615 137454173 2558 True 1138.0 2639 92.1090 1 2623 3 chr7A.!!$R1 2622

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
569 647 0.313672 GAAGGAATTGCACGCACCAA 59.686 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2178 0.179111 ACCGCTCGTCCACACATATG 60.179 55.0 0.0 0.0 0.0 1.78 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 3.408634 TGGATACTAGCGTGATGATCGA 58.591 45.455 0.00 0.00 37.61 3.59
104 105 3.252215 CGCCGAGCCATAAAATTATTCCA 59.748 43.478 0.00 0.00 0.00 3.53
211 212 1.870402 TGACTTGTTGCACCACATACG 59.130 47.619 0.00 0.00 0.00 3.06
269 270 0.694771 GGGAGGAAAACCTACCCGTT 59.305 55.000 6.27 0.00 34.79 4.44
271 272 2.489619 GGGAGGAAAACCTACCCGTTTT 60.490 50.000 6.27 0.00 46.08 2.43
474 549 2.158549 AGGGAATTTGCTCCTGATAGCC 60.159 50.000 0.00 0.00 42.05 3.93
476 551 2.485479 GGAATTTGCTCCTGATAGCCGA 60.485 50.000 0.00 0.00 42.05 5.54
565 642 0.320334 TCGAGAAGGAATTGCACGCA 60.320 50.000 0.00 0.00 0.00 5.24
569 647 0.313672 GAAGGAATTGCACGCACCAA 59.686 50.000 0.00 0.00 0.00 3.67
570 648 0.968405 AAGGAATTGCACGCACCAAT 59.032 45.000 0.00 0.00 34.56 3.16
572 650 0.458370 GGAATTGCACGCACCAATCC 60.458 55.000 0.00 0.00 32.07 3.01
896 974 3.063510 GGAACGGGTATAAATAGGGGC 57.936 52.381 0.00 0.00 0.00 5.80
899 977 1.345415 ACGGGTATAAATAGGGGCGTG 59.655 52.381 0.00 0.00 0.00 5.34
1552 1644 3.853330 CGAGCGGCACCGACATTG 61.853 66.667 14.43 0.00 42.83 2.82
1601 1693 2.202878 TGTGCGGGCGAAGATAGC 60.203 61.111 0.00 0.00 0.00 2.97
1611 1703 1.355916 GAAGATAGCGGCGTCGTCT 59.644 57.895 12.58 11.56 38.89 4.18
1660 1752 2.892640 CGATGGGGTGCTTCGAGA 59.107 61.111 0.00 0.00 34.92 4.04
1672 1764 3.391160 TTCGAGACCGTGATCCGCG 62.391 63.158 0.00 0.00 37.05 6.46
1829 1940 4.688879 TGTGCGTCGAAGAATTTTCTGTAT 59.311 37.500 1.37 0.00 39.69 2.29
1883 1994 3.148412 CCGTATGATCAAATCCATGCCA 58.852 45.455 0.00 0.00 0.00 4.92
1951 2062 5.520288 CCGAAAAGAGAAAGATATGCTCGAA 59.480 40.000 0.00 0.00 33.98 3.71
1952 2063 6.406820 CGAAAAGAGAAAGATATGCTCGAAC 58.593 40.000 0.00 0.00 33.98 3.95
1953 2064 6.254589 CGAAAAGAGAAAGATATGCTCGAACT 59.745 38.462 0.00 0.00 33.98 3.01
1954 2065 7.432545 CGAAAAGAGAAAGATATGCTCGAACTA 59.567 37.037 0.00 0.00 33.98 2.24
1995 2108 7.010738 GTGCAGTACTGTACTAAACTTTTGTGA 59.989 37.037 29.98 0.00 41.90 3.58
2065 2178 5.463061 ACTCAATGGCGCAATAATAATTTGC 59.537 36.000 10.83 0.00 44.68 3.68
2092 2205 3.244579 GTGTGGACGAGCGGTAATTAATC 59.755 47.826 0.00 0.00 0.00 1.75
2109 2222 0.605589 ATCTCCTCCCAATCGATCGC 59.394 55.000 11.09 0.00 0.00 4.58
2246 2383 1.135199 ACGTCGATGACAAGCCGTTAT 60.135 47.619 12.58 0.00 32.09 1.89
2438 2575 0.531753 GCCCATCTCGAAGCTTCCTC 60.532 60.000 20.62 0.00 0.00 3.71
2509 2646 4.607239 ACATGGGCTTGATCTTCTGAAAT 58.393 39.130 0.00 0.00 0.00 2.17
2515 2652 5.240403 GGGCTTGATCTTCTGAAATATGGTC 59.760 44.000 0.00 0.00 0.00 4.02
2649 2786 3.464080 TCCAAGGAACCCCTGTCTAAAAA 59.536 43.478 0.00 0.00 43.48 1.94
2670 2807 6.442513 AAATTGGGAAGAAGATTCGATCAC 57.557 37.500 0.00 1.83 0.00 3.06
2710 2847 0.409484 AAGTTTGTGATGGGGGAGGG 59.591 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.865365 CGACAGAAAGGAGGAATGAAGTAC 59.135 45.833 0.00 0.00 0.00 2.73
63 64 3.059570 GGCGTTATCGATTCGATCATCAC 59.940 47.826 23.82 15.02 43.45 3.06
67 68 1.264826 TCGGCGTTATCGATTCGATCA 59.735 47.619 23.82 11.66 43.45 2.92
73 74 0.033504 ATGGCTCGGCGTTATCGATT 59.966 50.000 1.71 0.00 39.71 3.34
146 147 3.221389 CCCCGACGCCGAGGATAA 61.221 66.667 0.00 0.00 35.49 1.75
364 368 2.863137 GCACAGAGCTAGTACTCATTGC 59.137 50.000 0.00 0.04 39.26 3.56
474 549 2.106566 AGCTATCCATATCTGCCCTCG 58.893 52.381 0.00 0.00 0.00 4.63
476 551 1.558756 GCAGCTATCCATATCTGCCCT 59.441 52.381 10.17 0.00 43.20 5.19
512 587 0.673644 AATGTACAGCTGGGCGTGAC 60.674 55.000 19.93 6.45 0.00 3.67
899 977 0.615331 TGAGGTTCTGTGGAGATGCC 59.385 55.000 0.00 0.00 37.10 4.40
963 1041 2.139118 GCCAATCAGCTATTCCGTCTC 58.861 52.381 0.00 0.00 0.00 3.36
1140 1229 3.077519 AAAGACCTCCGGATCGCGG 62.078 63.158 3.57 14.38 0.00 6.46
1451 1540 1.202568 CCTGCACGATAGAAGGATGCA 60.203 52.381 0.00 0.00 43.70 3.96
1543 1635 1.074248 GGGGGTTCACAATGTCGGT 59.926 57.895 0.00 0.00 0.00 4.69
1601 1693 4.831307 CCGGAGAAGACGACGCCG 62.831 72.222 0.00 0.00 46.79 6.46
1660 1752 4.814294 GGAAGCGCGGATCACGGT 62.814 66.667 8.83 6.29 44.51 4.83
1748 1853 8.956446 TTTTCCCCTAGATTTTCTTGAATCTT 57.044 30.769 5.55 0.00 42.24 2.40
1883 1994 5.684704 TGAAACAACTGGTTCATCTCTCTT 58.315 37.500 6.08 0.00 45.85 2.85
1951 2062 4.030913 TGCACATTAGAACCCTAGCTAGT 58.969 43.478 19.31 0.67 0.00 2.57
1952 2063 4.100189 ACTGCACATTAGAACCCTAGCTAG 59.900 45.833 14.20 14.20 0.00 3.42
1953 2064 4.030913 ACTGCACATTAGAACCCTAGCTA 58.969 43.478 0.00 0.00 0.00 3.32
1954 2065 2.840651 ACTGCACATTAGAACCCTAGCT 59.159 45.455 0.00 0.00 0.00 3.32
1995 2108 6.516739 TTCTGATCACAAAGAGTACTCGAT 57.483 37.500 17.07 12.71 34.09 3.59
2065 2178 0.179111 ACCGCTCGTCCACACATATG 60.179 55.000 0.00 0.00 0.00 1.78
2092 2205 0.319383 CAGCGATCGATTGGGAGGAG 60.319 60.000 21.57 0.00 0.00 3.69
2438 2575 1.064505 CAACGGAGCACATAAGCCATG 59.935 52.381 0.00 0.00 40.78 3.66
2515 2652 9.599866 TTGACCATTATACACTCTACAAATCAG 57.400 33.333 0.00 0.00 0.00 2.90
2574 2711 5.563592 TGGCCATCATAGACTCCAAATATG 58.436 41.667 0.00 0.00 0.00 1.78
2649 2786 4.122776 CGTGATCGAATCTTCTTCCCAAT 58.877 43.478 0.00 0.00 39.71 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.